From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Nov 28 2009 - 18:02:52 CST
Hi Blake,
For some reason, your initial PDB file contains atom types rather than
atom names. That is throwing psfgen off.
Jerome
2009/11/27 Blake Mertz <jbmertz_at_email.arizona.edu>:
> I'm running into a problem with my setup for MD testing of a molecule
> fragment against some QM results that I've compiled. My situation is this:
> I've got my fragment and want to do a dihedral scan of a methyl group. The
> appropriate fixed atoms are prepped with their values in the occupancy
> field, and all of my atoms are in the intial positions I want them, so I
> really don't need psfgen to guess their coordinates. I've spent the last
> couple weeks trying to find some answers on namd-l, but haven't really run
> across anyone with the specific error "Warning: failed to set coordinate"
> for every atom in their molecule. Here are some short examples from my
> files, starting with the psfgen output:
>
> reading topology file
> /home/blake/Documents/NAMD/toppar/top_all22_prot_cmap.inp
>
>>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
>>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
> All comments to ADM jr. via the CHARMM web site: www.charmm.org
> parameter set discussion forum
>
> Created by CHARMM version 31 1
> cross-term entries present in topology definitions
> reading topology file
> /home/blake/Documents/NAMD/toppar/toppar_c35_c36/stream/toppar_all22_prot_retinol-C5-frag-redo.inp
>
> retinal/retinol and related model compounds
>
> Created by CHARMM version 32 1
> aliasing residue UNK to RTC5
> building segment C5
> disabling angle autogeneration
> disabling dihedral autogeneration
> reading residues from pdb file C5-p10-vmd.pdb
> extracted 1 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> reading coordinates from pdb file C5-p10-vmd.pdb for segment C5
> Warning: failed to set coordinate for atom CT UNK:1 C5
> Warning: failed to set coordinate for atom CT2 UNK:1 C5
> Warning: failed to set coordinate for atom CT2 UNK:1 C5
> Warning: failed to set coordinate for atom CT2 UNK:1 C5
> ...............
> Info: guessing coordinates for 36 atoms (14 non-hydrogen)
> Warning: failed to guess coordinates for 36 atoms
>
> My pdb file was generated in vmd, but here are the first few lines:
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 CT UNK X 1 -0.621 0.576 -2.166 1.00
> 0.00
> ATOM 2 CT2 UNK X 1 -1.811 0.043 -2.987 1.00
> 0.00
> ATOM 3 CT2 UNK X 1 -3.104 0.006 -2.177 1.00
> 0.00
>
> My topology file, which was modeled after Jan Saam's for retinal:
> !read rtf card append
> * retinal/retinol and related model compounds
> *
> 32 1
>
> RESI RTC5 0.00 ! retinal C5-methyl fragment,
> ! nomenclature from PDB based on retinol
> !
> GROUP
> ATOM C1 CT 0.00
> ATOM C2 CT2 -0.18
> ATOM H21 HA 0.09
>
> My pgn file:
> package require psfgen
> topology /home/blake/Documents/NAMD/toppar/top_all22_prot_cmap.inp
> #topology
> /home/blake/Documents/NAMD/toppar/toppar_c35_c36/stream/toppar_all22_prot_retinol.str
> topology
> /home/blake/Documents/NAMD/toppar/toppar_c35_c36/stream/toppar_all22_prot_retinol-C5-frag-redo.inp
> pdbalias residue UNK RTC5
> segment C5 {
> auto none
> pdb C5-p10-vmd.pdb
> }
> coordpdb C5-p10-vmd.pdb C5
> guesscoord
> writepdb test.pdb
> writepsf test.psf
>
> And output test.pdb:
> REMARK original generated coordinate pdb file
> ATOM 1 C1 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
> C
> ATOM 2 C2 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
> C
> ATOM 3 H21 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
> H
> ATOM 4 H22 RTC5X 1 0.000 0.000 0.000 -1.00 0.00 C5
> H
>
> Sorry for the long email, I just haven't been able to find any good answers
> to this so far, and am getting frustrated trying to figure it out myself.
> Any help is definitely appreciated.
>
> Blake Mertz
> --
> Research Assistant
> Department of Chemistry
> University of Arizona
>
> "Life is not easy for any of us. But what of that? We must have perseverance
> and above all confidence in ourselves. We must believe that we are gifted
> for something and that this thing must be attained." Marie Curie
>
> "Start by doing what's necessary; then do what's possible; and suddenly you
> are doing the impossible." St. Francis of Assissi
>
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